I (kind of) fixed mine by going to /home/<your username>/.mysql/ and renaming (or deleting) the workbench folder. All of your connections need to be re-entered, but it's worth it to get your database program back up and running. The only reason I'm saying this is, because this was the only way I could get mine to work, no other solutions on the internet worked for me. I'm using Ubuntu 12.04, but this should work on any other version of Ubuntu as well.